Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Abstract

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38–39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa – suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.

Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance

“…We further searched the NCBI web database using blastn , EAKF1_ch3804 was present in one complete genome of E. coli ST9286 from guinea fowl [46] while the other two markers were only found in E. albertii .…”

Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr-10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East

“…E. coli were found to have two-allele sequence types; ST2165 and ST7624. Although ST2165 was previously detected in colistin-resistant E. coli carrying mcr - 1 from residents of long-term-care facilities ( Giufrè et al, 2016 ), it was isolated elsewhere from chickens and store-bought produce ( Reid et al, 2020 ; Foster-Nyarko et al, 2021 ). To our knowledge, this is the first isolation of this sequence type from milk.…”

“…In the view of plasmid replicon types, we found that the three E. coli isolates belonging to ST2165 have plasmid replicon types; IncFIA, IncFIB, IncFII, and IncQ1. Likewise, Foster-Nyarko et al (2021) reported that the MDR isolates often co-carried large IncF plasmids like IncFIA, IncFIB, or IncFIC.…”

Similar Antimicrobial Resistance of Escherichia coli Strains Isolated from Retail Chickens and Poultry Farms

“…In addition, Hoek et al suggested that ST155 and ST10 were most often found in broiler farms (Van Hoek et al, 2018). Not surprisingly, ST155 was the most common in several reports (Foster-Nyarko et al, 2021;Nguyen et al, 2021). In addition, seven ST156 strains were found only on farms, and they may be hosts for the transmission of the carbapenem resistance gene bla NDM , as previously reported (Tang et al, 2019).…”